[gmx-users] Re: Umbrella Sampling - ligand

Justin A. Lemkul jalemkul at vt.edu
Thu Mar 1 13:48:42 CET 2012

Steven Neumann wrote:
> Dear Gmx Users, Dear Justin,
> I run Umbrella Sampling for my ligand pulling using Justin's 
> Tutorial. Please, see attached my  histogram and PMF profile.
> I know it requires more sampling around distance from 0.8 to 2.5 nm.
> 1) Will more sampling affect the final deltaG which is now around -7.2 
> kcal/mol ? The profile will be more smooth surely... but the value will 
> stay the same I think.

You need more sampling in the region already stated (since there is none there). 
  Otherwise, things look fine.

> 2) Did I run too many simulations as histogram is very dense? Does it 
> have any effect or it is better to stay like this?

You have some windows where the histograms are almost coincident.  I'd 
investigate why that is, because I'm assuming you didn't intend different 
windows to be redundant.  I don't think there's any harm, but you probably ran 
more windows than is necessary.


> Please, if you have any more suggestions, I will appreciate.
> Thank you,
> Steven
> ------------------------------------------------------------------------
> ------------------------------------------------------------------------


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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